This proposal in response to RFA-RR-10-005 leverages a new collaboration between Dr. Skip Virgin and Dr. Dan Barouch to define the role of the enteric microbiome, virome, and metagenome in the health of SIV-infected and uninfected macaques. Little is known about the metagenome of the macaque intestine and its relationship to disease, yet understanding intestinal 'ecology' is essential for defining the basic biology and immunology of the intestine. This is critical for understanding how to diagnose precious animals, vaccinate against mucosal lentivirus challenge, and the mechanisms driving progression to AIDS. In a cross-sectional study of 39 macaques we used deep sequencing and metagenomic analysis to find at least 19 new enteric macaque viruses (indicating that the macaque 'virome' is extensive) and significant differences in the microbiome and virome in SIV-infected compared to uninfected animals. Thus we have a unique opportunity to analyze interactions between lentivirus infection and the enteric microbiome/virome in macaques. The significance of this proposal will be defining: (i) the fundamental nature of, and effects of SIV on, the microbiome/virome; (ii) the role of many newly discovered viruses and changes in the microbiome in disease, and (iii) whether the microbiome/virome contributes to intestinal leakage and systemic immune activation during SIV infection. We will address these cross-disciplinary questions by linking expertise in macaque health and lentivirus infection and vaccination (Barouch/Carville/Mansfeild) with expertise in relating the microbiome/virome to intestinal pathology, virus discovery, and metagenomics (Virgin/Wang/ Zhao/Handley). This team can rapidly generate data that may fundamentally change approaches to the use of primates in biomedical research. Since little is known about macaque metagenomics, we will combine unbiased longitudinal discovery experiments with testing of our primary hypothesis that vaccination will block the effects of SIV on the microbiome and virome. The impact of our studies could come from: (i) changes in veterinary care, (ii) a new paradigm for the source of systemic immune activation during SIV infection, and (iii) improved fundamental understanding of the relationship between intestinal ecology and the immune system. We will therefore address the following Aims: Aim 1) Define the relationship between the macaque microbiome and virome and enteric disease. Aim 2) Define the impact of SIV infection on the enteric microbiome/virome.